molcas_maker.py

#!/usr/bin/env python

# Script by Jogvan to make molcas input files from xyz
# Only removed some submit stuff (arnfinn)

import os
import argparse as ap

parser = ap.ArgumentParser(description='LoProp job submitter 0.1b')

parser.add_argument('-xyz', '--xyz', dest='xyzfile', metavar='XYZ_FILE',
                    help='''the name of the xyz input file that contains the
                            molecule.''')

parser.add_argument('--method', dest='method', metavar='METHOD',
                     default='DFT', choices=['DFT', 'HF'],
                     help='''Choose QM method. Valid choices are
                             %(choices)s. If you use DFT then you can also
                             specify the xc-functional using the
                             --xcfun option. [default: %(default)s]''')

parser.add_argument('--basis', dest='basis', metavar='BASISSET',
                     default='A-AUG-CC-PVDZ',
                     help='''Specify basis set. [default: %(default)s]''')

parser.add_argument('--xcfun', dest='xcfun', default='B3LYP',
                     metavar='XCFUN',
                     help='''Specify xc-functional. [default: %(default)s]''')

parser.add_argument('--bond-midpoints', dest='bonds', action='store_true',
                    default=False,
                    help='''Also calculate parameters on bond midpoints.
                            [default: %(default)s]''')

parser.add_argument('--charge', dest='charge', metavar='CHARGE',
                     default=0, type=int,
                     help='''Specify basis set. [default: %(default)s]''')

args = parser.parse_args()

if not args.xyzfile:
    exit('You must specify a .mol input file.')

if args.xyzfile[-4:] == '.xyz':
    xyzfile = args.xyzfile[:-4]
else:
    xyzfile = args.xyzfile

if not os.path.isfile('{}.xyz'.format(xyzfile)):
    exit('{}.xyz not found.'.format(xyzfile))

if args.method == 'DFT':
    method = 'KSDFT\n' + args.xcfun
elif args.method == 'HF':
    method = ''
else:
    exit('Invalid QM method for force field calculation.')

if args.bonds:
    bmids = ''
else:
    bmids = 'BONDS\n0.0\n'

if args.basis == "2":
    basis = "A-AUG-CC-PVDZ"
else:
    basis = args.basis

input = ('&GATEWAY &END\n' +
         'TITLE\n' +
         'Generated by subloprop 0.1b\n' +
         'COORD\n' +
         '{0}.xyz\n'.format(xyzfile) +
         'BASIS\n' +
         '{0}\n'.format(basis) +
         'GROUP\n' +
         'C1\n' +
         'END OF INPUT\n' +
         '&SEWARD &END\n' +
         'MULT\n' +
         '2\n' +
         'CHOL\n' +
         'END OF INPUT\n' +
         '&SCF &END\n' +
         'CHARGE\n' +
         '{0}\n'.format(args.charge) +
         'CHOL\n' +
         '{0}\n'.format(method) +
         'END OF INPUT\n' +
         '&LOPROP &END\n' +
         'MPPROP\n' +
         '2\n' +
         '{0}'.format(bmids) +
         'END OF INPUT\n')
finp = open('{0}.inp'.format(xyzfile), 'w')
finp.write(input)
finp.close()